MolNFT v1 · #123114 · protein
Mycobacterium tuberculosis dihydrofolate reductase complexed with beta- NADPH and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-YL)PROP-2-yn-1- yl)-4'-methoxy-[1,1'-B iphenyl]-4-carboxylic acid (UCP1106)
5JA3: “Mycobacterium tuberculosis dihydrofolate reductase complexed with beta- NADPH and…”. X-ray diffraction, 2 ligands (NDP, U06), 8 pockets (best druggability 0.83). MolNFT v1 #123114 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JA3
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P9WNX0
- Ligands
- NDP, U06
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 21% helix, 34% strand | P9WNX0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- U06 · 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-4-methoxy-phenyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.83 | 0.84 | 101 | NDP, U06 |
| 2 | 632 | 0.74 | 0.80 | 63 | NDP, U06 |
| 3 | 523 | 0.73 | 0.82 | 49 | NDP, U06 |
| 4 | 501 | 0.72 | 0.81 | 45 | NDP, U06 |
| 5 | 103 | 0.40 | 0.77 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 562 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 526 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 171 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5JA3 · Mycobacterium tuberculosis Dihydrofolate Reductase complexed with beta- NADPH and… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WNX0 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P9WNX0) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P9WNX0
- Elsewhere: RCSB PDB 5JA3 · PDBe 5JA3 · UniProt P9WNX0
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